Understanding the transport of dissolved organic carbon (DOC) and nitrogen (N) as water flows through headwater basins is important for predicting downstream water quality. With increased recognition of climatic impact on nutrient transport, more studies are needed in headwater basins experiencing a Mediterranean-type climate, such as those of the Sierra Nevada, California. We analyzed water samples collected over 5 years from eight low-order and mixed-conifer watersheds to elucidate the temporal variation of water chemistry and evaluate their responses to prolonged drought and low-intensity forest thinning. We observed higher stream DOC concentrations in October compared to other months within water years prior to drought and thinning, suggesting the importance of antecedent moisture conditions on seasonal C export. In unthinned watersheds, stream DOC concentrations were lower (62%) and DOC aromaticity was higher (68 and 92%, depending on the index used) during drought compared to non-drought years. In thinned watersheds during drought years, stream water had higher DOC concentrations (66–94% in three consecutive years following thinning) and dissolved inorganic N (24%, in the third year following thinning) compared to unthinned watersheds during drought. Additionally, lower stream DOC concentrations were found in watersheds with higher elevations and lower drainage densities in the year with near-average precipitation; however, these correlations were not significant in years with greater or extremely low precipitation. Taken together, our results suggest that stream concentrations of DOC and dissolved N in Mediterranean headwater basins are extremely variable over time due to the high temporal climatic variabilities and periodic management practices.